MGnify — EMBL-EBI's metagenomics resource: public microbiome studies, the biome vocabulary they are classified under, and the ~57,000 MAGs and isolate genomes in its species-level genome catalogues, with completeness, contamination and GTDB taxonomy for each.
Setup
Choose your client, copy the config, then fill in any required environment variables.
claude mcp add --transport http mgnify https://gateway.pipeworx.io/mgnify/mcp~/.codex/config.toml
[mcp_servers.mgnify]
url = "https://gateway.pipeworx.io/mgnify/mcp"
# codex mcp add mgnify --url https://gateway.pipeworx.io/mgnify/mcp~/.cursor/mcp.json
{
"mcpServers": {
"mgnify": {
"url": "https://gateway.pipeworx.io/mgnify/mcp"
}
}
}.vscode/mcp.json
{
"servers": {
"mgnify": {
"type": "http",
"url": "https://gateway.pipeworx.io/mgnify/mcp"
}
}
}~/.gemini/settings.json
{
"mcpServers": {
"mgnify": {
"httpUrl": "https://gateway.pipeworx.io/mgnify/mcp"
}
}
}claude_desktop_config.json · Customize › Connectors › Add custom connector
{
"mcpServers": {
"mgnify": {
"command": "npx",
"args": [
"-y",
"mcp-remote",
"https://gateway.pipeworx.io/mgnify/mcp"
]
}
}
}.trae/mcp.json
{
"mcpServers": {
"mgnify": {
"url": "https://gateway.pipeworx.io/mgnify/mcp"
}
}
}